The thing about Famke and Sophie is that they weren't really allowed to define Jean as a 3D character. In those first 3 X-Men films, Jean isn't really developed beyond 'The X-Woman with telepathy". She's less a character in her own right and more of a tool to soften Logan's heart and in X3, a plot device to drive the story foward. We never really learn anything about Jean beyond the bare essentials.
Eh. I get that this is the perception, but just because that's what people remember...that's not the reality of the character as she's actually presented.
Jean is the one who introduces the X-gene concept in X-MEN and educates the public via the senate hearing. We see that she's their public face, we learn that she's a doctor and a teacher at the school, we see that she has a sense of humor, learn that she's hesitant about testing her limits but capable of doing so...we learn that she can be tempted but make moral decisions...she is far more, even as a supporting character, than merely "The X-Woman with telepathy".
In XMA, we are introduced to pre- X-Men Jean and rather than use this opportunity to create a formative arc for her, they make her ancillary, along with all of the other X-Men. Once again, we know nothing about Jean beyond the fact that she's telepathic and has a crush on Scott. Introspective scenes like this should have never been deleted
That she is telepathic and has a crush on Scott is definitely not all we learn about Jean. Much like in prior films, we learn that she has issues controlling and bearing her power, we learn that she can/is evolving, etc. In APOCALYPSE, we see a more traditional young adult approach to the conflict; the level of fear she has over it's emergence, the anxiety it produces, and her doubts that she is going to get better. We find out that not only can she reads minds, but she can also essentially feel what other people do, and we see the impact this has on her as well. We see her use this compassionately, IE the chopper sequence with Scott, and later with Logan.
I'm not saying the deleted scenes shouldn't have been in the movie. They're fun and there's a tidbit here and there, but what do we actually learn about the characters in these few deleted scenes that isn't conveyed elsewhere in the movie? That they like to go to the mall? That Jean and Scott met once and they're both kinda freaks (the movie clearly conveys this in other scenes)? That Jean likes to watch birds?
It's not like there aren't scenes of Jean and Scott bonding in the films as they exist, they're just not in as much of a "young romance" style, and they're actually tied into the main storyline in the middle of the action instead of separate sequences. I'm not saying scenes like that might not have humanized them a bit, but there's not really much character development to speak of in these specific sequences. Nor is there much in the way of story that isn't extraneous. That's likely why they were cut in the first place.
Jean Grey, as a character, tends, even in the source material, to be defined by her core conflicts, as most characters are. Her core conflict is her ability to evolve and grow in power, namely her issues with maintaining control. These things were pretty clearly drawn over not only the first three X-Men films, but also the last two.
In regards to Jean, the audience struggles to care about her struggle.
I can't speak for everyone, but I disagree. The film positions her control issues as similar to say, the struggles someone might experience battling mental illness. I found Jean very relatable in Dark Phoenix, considerably moreso than in say, X3, and arguably the first two X-Films. Her personal struggles, and the way people respond to them, is pretty much the only reason the movie works on any level.
Rather, Kinberg uses whatever emotional tether there is left to the First Class characters to frame Jean's actions in a way that people might care i.e Killing Mystique. But ehh, Raven's character declined after DOFP so most people did not care[/spoiler]
Mystique's death is part of a chain of events. Jean also injures Quicksilver, threatens police, soldiers, and effectively tortures her mentor and Magneto.
Mystique's death is central to the emotional schism the X-Men go through, but Jean's transformation and conflict almost entirely revolves around the idea that she is struggling, but may not be broken. Mystique's death, while providing stakes, is not the central way the film portrays Jean/The Phoenix. It is Jean and the other characters' response to Jean's predicament that is the lens we see everything through.
I do think Scott and Jean and their various relationship conflicts need to be more central to the MCU X-Men, and I'm all for endless melodrama. That's classic X-Men stuff. There's a balancing act ahead, it'll be interesting to see how they handle it.